The adaptive immune response starts with recognition of peptide antigens presented by class II molecules of the Major Histocompatibility Complex (MHC). Two outstanding features of these molecules are their polymorphism and the ability of each allele to bind a large panoply of peptides. The long-term goal of the research proposed here is to understand the function of the human class II MHC molecule HLA-DR in antigen presentation and the role of polymorphism therein. With a better understanding, progress can be made in two practical areas where HLA-DR plays a significant role, vaccination and transplantation. The short-term goal is to examine peptide binding at a basic level with the goal of understanding the process to the point that rational approaches to pathogen epitope identification can be established. Our model is that we are dissecting a complex system where one interaction is affected by other interactions. Our preliminary data indicates that this cooperativity between interactions is indeed an important aspect of the binding mechanism. In Aim 1 we investigate the phenomenon of cooperativity in more detail. We will determine whether the cooperativity we have observed in peptide residues that contact solvent extend to other residues. In Aim 2 we analyze further aspects of peptide binding including the possible role of hydrophobic nucleation sites and additional stability conferred through flanking residues. In Aim 3, the information gained in the two previous aims will be analyzed in the context of a hypothesis that there is a relation between intrinsic stability, cooperativity and a conformational change that allows stable binding of peptides of different apparent affinities. This is what allows the binding of a large number of peptides. Peptide binding takes place in the presence of an adjunct molecule, HLA-DM, which promotes the exchange of peptides. In Aim 4 we will determine structural characteristics that influence DM-mediated peptide exchange, thus providing insight as to what is an acceptable peptide for a particular HLA-DR allele. This may also lead to an understanding of the mechanism by which HLA-DM functions. Our model for this interaction is that HLA-DM puts the HLA-DR in a conformation in which the overall peptide-binding properties are changed and peptides interact based solely on their affinity.